Gene expression

Illumina/Solexa whole transcriptome sequencing provides information about gene expression, as well as nucleotide sequence. The more copies of a specific transcript in an RNA isolation, the more times that transcript will be sequenced. Transcript abundance correlates directly with gene expression levels.

Tissues used in expression analysis

Transcriptome libraries from shoots, roots, and nodules of Chamaecrista fasciculata plants at different stages of development were used for Illumina/Solexa sequencing. Before sequencing, mRNA was purified from the total RNA. You can get more information about the stages by downloading the linked PowerPoint slides. Shoot, root, and nodule libraries(PowerPoint 2007 (.pptx) 14MB Jan19 09)

JMP Genomics exercise to get you thinking about gene expression

JMP Genomics is a statistical software package that lets you look for gene expression patterns. The two links that follow provide the directions and data needed to visualize patterns in gene expression among the different Chamaecrista tissue types. Work through this exercise before you go on to plan your own strategy for working with the expression data. The software is available for all faculty and students in the Biology Department. It is currently on the machines in CMC 109 and the Biology Computer Lab. As a student in the class, you can download your own copy from the COLLAB server folder (Departments/Biology) onto a Windows machine.

UAG - Stop and Reflect

Explain how the number of reads of a given sequence provides you with useable information about gene expression. Describe two other ways you could determine the level of expression of specific genes. Respond in your journal

Asking questions with expression data

What is the overall pattern of gene expression for the shoot transcriptome?

Using the youngest shoot library, can you rank the genes based on expression and plot your results?

What happens if you then plot the data for the other shoot libraries? How do they compare to each other?

Can you compare expression patterns in roots, shoots, and nodules? How might you organize and present the data?

If you worked on candidate genes, can you use that information to look at expression patterns of specific genes as a function of tissue type and developmental stage?

UAG - Stop and Reflect

Develop a hypothesis about shoot development using expression data. Respond in your journal

UAG - Stop and Reflect

What does it mean to assemble the transcriptome? Record how and why sequence data is assembled. Respond in your journal

UAG - Stop and Reflect

Why might you need the files with the assembly data if you have the Blast Chamaecrista site available to you? Respond in your journal